Boss Zeta plays during encounters with Zeta Metroids. It opens with a shrill stinger, followed by a low choir reminiscent of the Chozo temple themes from Metroid Prime and Metroid: Zero Mission. The rest of the track is an exciting high-energy battle theme, with a more cinematic flair compared to Boss Alpha and Boss Gamma due to featuring an dramatic brass melody in lieu of the standard electronic synths. It can be heard here: [1]

Boss Zeta appears to be a largely original composition, not based upon any of the songs composed by Ryoji Yoshitomi for Metroid II: Return of Samus. However, the opening stinger is notably similar to the original Metroidbattle theme from Return of Samus. This may have been a deliberate reference by Daisuke Matsuoka, although this is not confirmed.